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protocols::rna::denovo::movers::RNA_DeNovoProtocolMover Class Reference

#include <RNA_DeNovoProtocolMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_DeNovoProtocolMover:
Inheritance graph
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Public Member Functions

 RNA_DeNovoProtocolMover ()
 
 ~RNA_DeNovoProtocolMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options () const
 
core::import_pose::RNA_DeNovoParametersCOP rna_params () const
 
void set_fasta_files (utility::vector1< std::string > const &fasta_files)
 
void set_input_pdbs (utility::vector1< std::string > const &input_pdbs)
 
void set_input_silent_files (utility::vector1< std::string > const &input_silent_files)
 
void set_sequence_strings (utility::vector1< std::string > const &sequence_strings)
 
void set_minimize_rna (bool const minimize_rna)
 
void set_helical_substructs (utility::vector1< std::string > const &helical_substructs)
 
void set_dock_chunks (utility::vector1< std::string > const &dock_chunks)
 
void set_input_initialization_pdbs (utility::vector1< std::string > const &input_initialization_pdbs)
 
void set_align_pdb (std::string const &align_pdb)
 
void set_nstruct (Size const nstruct)
 
void set_silent_file (std::string const &silent_file)
 
void de_novo_setup_from_command_line ()
 
void de_novo_setup_from_options (utility::options::OptionCollection const &opts)
 
void de_novo_setup_from_tag (utility::tag::TagCOP const &tag)
 
void set_protocol_options (core::import_pose::options::RNA_DeNovoProtocolOptionsOP const &protocol_options)
 
void set_residue_type_set (core::chemical::ResidueTypeSetCOP const &rts)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void list_options_read (utility::options::OptionKeyList &opts)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Types

using Size = core::Size
 

Private Member Functions

void initialize_scorefxn (core::pose::Pose &pose)
 
void initialize_sequence_information (int const offset, bool const edensity_mapfile_provided, bool const rna_protein_docking, bool const virtual_anchor_provided, bool const cutpoint_open_provided, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &possible_cutpoint_open_numbering, core::pose::full_model_info::FullModelParametersOP &full_model_parameters, utility::vector1< core::Size > &cutpoint_open_in_full_model)
 
void check_secstructs (bool const modeling_with_density, bool const rna_protein_docking, std::string const &sequence, core::pose::rna::RNA_SecStruct const &secstruct, core::pose::rna::RNA_SecStruct const &secstruct_general)
 
void input_numbering_setup (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_res_resnum_and_chain, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_silent_res_resnum_and_chain, std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< int > > &resnum_list, utility::vector1< core::Size > &input_res_initialize, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res)
 
void input_pdb_numbering_setup (std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res, utility::vector1< utility::vector1< int > > &resnum_list, utility::vector1< core::Size > &input_res_user_defined, Size &input_res_user_defined_count)
 
void input_initialization_pdb_numbering_setup (std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_initialization_res)
 
void input_silent_numbering_setup (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_silent_res_resnum_and_chain, std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &input_res_user_defined, core::Size const &input_res_user_defined_count, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res, utility::vector1< utility::vector1< int > > &resnum_list)
 
void setup_obligate_pair (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_res, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< utility::vector1< int > > const &resnum_list, core::pose::rna::RNA_SecStruct const &secstruct, core::pose::rna::RNA_SecStruct const &secstruct_general, utility::vector1< core::Size > const &cutpoint_open_in_full_model, utility::vector1< core::Size > &obligate_pair, utility::vector1< std::string > &obligate_pair_explicit, utility::vector1< core::Size > &domain_map)
 
void initial_pose_setup (std::string const &in_path, bool const lores_sfxn_provided, bool const native_provided, bool const edensity_mapfile_provided, bool const working_native_provided, std::string const &working_native, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &working_res, core::pose::Pose &full_pose, bool &is_rna_and_protein)
 
void constraint_setup (bool const constraint_file_provided, std::string const &constraint_file, utility::vector1< core::Size > const &working_res, core::pose::Pose &full_pose)
 
void refine_working_obligate_pairs (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &remove_obligate_pair_rc, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &obligate_pair, utility::vector1< std::string > &obligate_pair_explicit, utility::vector1< core::Size > const &working_res, utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs)
 
void setup_working_chain_connections (utility::vector1< std::string > const &chain_connections, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &working_res, utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > &working_chain_connections)
 
void setup_pairing_sets (utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, core::pose::rna::RNA_BasePairList &rna_pairing_list, utility::vector1< utility::vector1< core::Size > > &working_obligate_pair_sets, utility::vector1< utility::vector1< core::Size > > &working_stem_pairing_sets)
 
void setup_ft_from_silent (bool const ft_from_silent_provided, std::string const &ft_silent_file, bool const tag_provided, utility::vector1< std::string > const &tag, bool &use_fold_tree_from_silent_file, core::kinematics::FoldTree &fold_tree_from_silent_file)
 
void setup_final_res_lists (utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &cutpoint_open_in_full_model, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_chi_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_jump_res_rc, bool const minimize_rna_specified, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &syn_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &anti_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &block_stack_above_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &block_stack_below_rc, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters)
 
utility::vector1< core::Sizeworking_res_map (utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res, bool const leave_out_last_working_residue=false) const
 
std::string working_res_map (std::string const &seq, utility::vector1< core::Size > const &working_res, bool const annotations_in_brackets=true) const
 
core::pose::rna::RNA_SecStruct working_res_map (core::pose::rna::RNA_SecStruct const &seq, utility::vector1< core::Size > const &working_res) const
 
void get_seq_and_resnum (std::string const &pdb, std::string &seq, utility::vector1< int > &resnum, utility::vector1< char > &chain, utility::vector1< std::string > &segid) const
 
std::string get_silent_seq (std::string const &silent_file) const
 
std::tuple< utility::vector1
< int >, utility::vector1
< char >, utility::vector1
< std::string > > 
get_silent_resnum (std::string const &silent_file) const
 
bool already_listed_in_obligate_pair (utility::vector1< core::Size > const &new_pair, utility::vector1< core::Size > const &obligate_pair) const
 
bool already_listed_in_obligate_pair (utility::vector1< Size > const &new_pair, utility::vector1< Size > const &obligate_pair, utility::vector1< Size > const &obligate_pair_explicit) const
 
void update_working_obligate_pairs_with_stems (utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::Size > const &working_input_res) const
 
core::pose::PoseOP get_native_pose ()
 
void add_chem_shift_info (core::pose::Pose &not_very_const_pose) const
 

Private Attributes

core::import_pose::options::RNA_DeNovoProtocolOptionsOP options_
 
core::import_pose::RNA_DeNovoParametersOP rna_params_
 
core::chemical::ResidueTypeSetCOP rsd_set_
 
core::pose::PoseOP pose_
 
core::pose::PoseOP native_pose_
 
utility::vector1< std::string > fasta_files_
 
utility::vector1< std::string > input_pdbs_
 
utility::vector1< std::string > input_silent_files_
 
utility::vector1< std::string > sequence_strings_
 
bool minimize_rna_
 
bool minimize_rna_has_been_specified_ = false
 
utility::vector1< std::string > helical_substructs_
 
utility::vector1< std::string > dock_chunks_
 
utility::vector1< std::string > input_initialization_pdbs_
 
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP vdw_grid_
 
RNA_FragmentMonteCarloOP rna_fragment_monte_carlo_
 
core::scoring::ScoreFunctionOP denovo_scorefxn_
 
core::scoring::ScoreFunctionOP hires_scorefxn_
 
std::list< core::Realall_lores_score_final_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::RNA_DeNovoProtocolMover ( )
protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::~RNA_DeNovoProtocolMover ( )
overridedefault

Member Function Documentation

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::add_chem_shift_info ( core::pose::Pose not_very_const_pose) const
private
bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::already_listed_in_obligate_pair ( utility::vector1< core::Size > const &  new_pair,
utility::vector1< core::Size > const &  obligate_pair 
) const
private
bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::already_listed_in_obligate_pair ( utility::vector1< Size > const &  new_pair,
utility::vector1< Size > const &  obligate_pair,
utility::vector1< Size > const &  obligate_pair_explicit 
) const
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply ( core::pose::Pose )
overridevirtual
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::check_secstructs ( bool const  modeling_with_density,
bool const  rna_protein_docking,
std::string const &  sequence,
core::pose::rna::RNA_SecStruct const &  secstruct,
core::pose::rna::RNA_SecStruct const &  secstruct_general 
)
private
moves::MoverOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::constraint_setup ( bool const  constraint_file_provided,
std::string const &  constraint_file,
utility::vector1< core::Size > const &  working_res,
core::pose::Pose full_pose 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_command_line ( )
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options ( utility::options::OptionCollection const &  opts)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag ( utility::tag::TagCOP const &  tag)
moves::MoverOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

core::pose::PoseOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_native_pose ( )
inlineprivate

References native_pose_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_seq_and_resnum ( std::string const &  pdb,
std::string &  seq,
utility::vector1< int > &  resnum,
utility::vector1< char > &  chain,
utility::vector1< std::string > &  segid 
) const
private
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_silent_resnum ( std::string const &  silent_file) const
private
std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_silent_seq ( std::string const &  silent_file) const
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup ( std::string const &  in_path,
bool const  lores_sfxn_provided,
bool const  native_provided,
bool const  edensity_mapfile_provided,
bool const  working_native_provided,
std::string const &  working_native,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > const &  working_res,
core::pose::Pose full_pose,
bool is_rna_and_protein 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_scorefxn ( core::pose::Pose pose)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information ( int const  offset,
bool const  edensity_mapfile_provided,
bool const  rna_protein_docking,
bool const  virtual_anchor_provided,
bool const  cutpoint_open_provided,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  possible_cutpoint_open_numbering,
core::pose::full_model_info::FullModelParametersOP full_model_parameters,
utility::vector1< core::Size > &  cutpoint_open_in_full_model 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_initialization_pdb_numbering_setup ( std::string const &  sequence,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > &  input_initialization_res 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_numbering_setup ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  input_res_resnum_and_chain,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  input_silent_res_resnum_and_chain,
std::string const &  sequence,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > &  input_res,
utility::vector1< utility::vector1< int > > &  resnum_list,
utility::vector1< core::Size > &  input_res_initialize,
utility::vector1< utility::vector1< core::Size > > &  helical_substruct_res,
utility::vector1< core::Size > &  dock_chunks_res 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_pdb_numbering_setup ( std::string const &  sequence,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > &  input_res,
utility::vector1< utility::vector1< core::Size > > &  helical_substruct_res,
utility::vector1< core::Size > &  dock_chunks_res,
utility::vector1< utility::vector1< int > > &  resnum_list,
utility::vector1< core::Size > &  input_res_user_defined,
Size input_res_user_defined_count 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_silent_numbering_setup ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  input_silent_res_resnum_and_chain,
std::string const &  sequence,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > const &  input_res_user_defined,
core::Size const &  input_res_user_defined_count,
utility::vector1< core::Size > &  input_res,
utility::vector1< utility::vector1< core::Size > > &  helical_substruct_res,
utility::vector1< core::Size > &  dock_chunks_res,
utility::vector1< utility::vector1< int > > &  resnum_list 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::list_options_read ( utility::options::OptionKeyList &  opts)
static
std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::mover_name ( )
static
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::options ( ) const
inline

References options_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::chemical::FA_STANDARD.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::refine_working_obligate_pairs ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  remove_obligate_pair_rc,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > const &  obligate_pair,
utility::vector1< std::string > &  obligate_pair_explicit,
utility::vector1< core::Size > const &  working_res,
utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs 
)
private
core::import_pose::RNA_DeNovoParametersCOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rna_params ( ) const
inline

References rna_params_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_align_pdb ( std::string const &  align_pdb)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_dock_chunks ( utility::vector1< std::string > const &  dock_chunks)
inline

References dock_chunks_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_fasta_files ( utility::vector1< std::string > const &  fasta_files)
inline

References fasta_files_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_helical_substructs ( utility::vector1< std::string > const &  helical_substructs)
inline

References helical_substructs_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_input_initialization_pdbs ( utility::vector1< std::string > const &  input_initialization_pdbs)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_input_pdbs ( utility::vector1< std::string > const &  input_pdbs)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_input_silent_files ( utility::vector1< std::string > const &  input_silent_files)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_minimize_rna ( bool const  minimize_rna)
inline
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_nstruct ( Size const  nstruct)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_protocol_options ( core::import_pose::options::RNA_DeNovoProtocolOptionsOP const &  protocol_options)
inline

References options_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_residue_type_set ( core::chemical::ResidueTypeSetCOP const &  rts)
inline

References rsd_set_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_sequence_strings ( utility::vector1< std::string > const &  sequence_strings)
inline

References sequence_strings_.

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_silent_file ( std::string const &  silent_file)
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_final_res_lists ( utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  cutpoint_open_in_full_model,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  extra_minimize_res_rc,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  extra_minimize_chi_res_rc,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  output_jump_res_rc,
bool const  minimize_rna_specified,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  syn_chi_rc,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  anti_chi_rc,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  block_stack_above_rc,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  block_stack_below_rc,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_ft_from_silent ( bool const  ft_from_silent_provided,
std::string const &  ft_silent_file,
bool const  tag_provided,
utility::vector1< std::string > const &  tag,
bool use_fold_tree_from_silent_file,
core::kinematics::FoldTree fold_tree_from_silent_file 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_obligate_pair ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  extra_minimize_res,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< utility::vector1< int > > const &  resnum_list,
core::pose::rna::RNA_SecStruct const &  secstruct,
core::pose::rna::RNA_SecStruct const &  secstruct_general,
utility::vector1< core::Size > const &  cutpoint_open_in_full_model,
utility::vector1< core::Size > &  obligate_pair,
utility::vector1< std::string > &  obligate_pair_explicit,
utility::vector1< core::Size > &  domain_map 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_pairing_sets ( utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &  working_stems,
utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs,
core::pose::rna::RNA_BasePairList rna_pairing_list,
utility::vector1< utility::vector1< core::Size > > &  working_obligate_pair_sets,
utility::vector1< utility::vector1< core::Size > > &  working_stem_pairing_sets 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_working_chain_connections ( utility::vector1< std::string > const &  chain_connections,
core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters,
utility::vector1< core::Size > const &  working_res,
utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > &  working_chain_connections 
)
private
void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::update_working_obligate_pairs_with_stems ( utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs,
utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &  working_stems,
utility::vector1< core::Size > const &  working_input_res 
) const
private
vector1< Size > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map ( utility::vector1< core::Size > const &  vec,
utility::vector1< core::Size > const &  working_res,
bool const  leave_out_last_working_residue = false 
) const
private
std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map ( std::string const &  seq,
utility::vector1< core::Size > const &  working_res,
bool const  annotations_in_brackets = true 
) const
private
core::pose::rna::RNA_SecStruct protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map ( core::pose::rna::RNA_SecStruct const &  seq,
utility::vector1< core::Size > const &  working_res 
) const
private

Member Data Documentation

std::list< core::Real > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::all_lores_score_final_
private
core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::denovo_scorefxn_
private
utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::dock_chunks_
private

Referenced by set_dock_chunks().

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::fasta_files_
private

Referenced by set_fasta_files().

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::helical_substructs_
private

Referenced by set_helical_substructs().

core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::hires_scorefxn_
private
utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_initialization_pdbs_
private
utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_pdbs_
private
utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_silent_files_
private
bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::minimize_rna_
private

Referenced by set_minimize_rna().

bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::minimize_rna_has_been_specified_ = false
private

Referenced by set_minimize_rna().

core::pose::PoseOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::native_pose_
private

Referenced by get_native_pose().

core::import_pose::options::RNA_DeNovoProtocolOptionsOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::options_
private

Referenced by options(), and set_protocol_options().

core::pose::PoseOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::pose_
private
RNA_FragmentMonteCarloOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rna_fragment_monte_carlo_
private
core::import_pose::RNA_DeNovoParametersOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rna_params_
private

Referenced by rna_params().

core::chemical::ResidueTypeSetCOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rsd_set_
private

Referenced by set_residue_type_set().

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::sequence_strings_
private

Referenced by set_sequence_strings().

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::vdw_grid_
private

The documentation for this class was generated from the following files: